rs7872903

Positions:

• chr9-133619170-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564021.1(ENSG00000261018):​n.114-5496A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,142 control chromosomes in the GnomAD database, including 7,377 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7377 hom., cov: 32)
• Consequence: ENST00000564021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000564021.1	n.114-5496A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41930 AN: 152024 Hom.: 7360 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00982

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.247

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41979 AN: 152142 Hom.: 7377 Cov.: 32 AF XY: 0.265 AC XY: 19698 AN XY: 74384

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00965

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.244

Alfa AF: 0.225 Hom.: 5788

Bravo AF: 0.284

Asia WGS AF: 0.0760 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7872903; hg19: chr9-136484292;